genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden markov model基因组的关系和物种形成的人类、黑猩猩和大猩猩从隐马尔可夫模型合并的推断.pdfVIP

Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model 1* 2 2,3 2 Asger Hobolth , Ole F. Christensen , Thomas Mailund , Mikkel H. Schierup 1 Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America, 2 Bioinformatics Research Center, University of Aarhus, Aarhus, Denmark, 3 Department of Statistics, University of Oxford, Oxford, United Kingdom The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human–chimp–gorilla–orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human–chimp (4.1 6 0.4 million years), and fairly large ancestral effective population sizes (65,000 6 30,000 for the human–chimp ancestor and 45,000 6 10,000 for the human–chimp–gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, su